homing endonuclease

Although the origin and function of homing endonucleases is still being researched, the most established hypothesis considers them as selfish genetic elements,{{cite journal | author = Edgell DR | title = Selfish DNA: homing endonucleases find a home | journal = Curr Biol | volume = 19 | issue = 3 |date=February 2009 | pages = R115–R117 | pmid = 19211047 | doi = 10.1016/j.cub.2008.12.019| s2cid = 2380439 |doi-access=free | bibcode = 2009CBio...19.R115E }} similar to transposons, because they facilitate the perpetuation of the genetic elements that encode them independent of providing a functional attribute to the host organism.

Homing endonuclease recognition sequences are long enough to occur randomly only with a very low probability (approximately once every {{val|7|e=9|u=bp}}),{{cite journal | author = Jasin M | title = Genetic manipulation of genomonth with rare-cutting endonucleases | journal = Trends Genet | issue = 6 | pages = 224–8 |date=Jun 1996 | pmid = 8928227 | doi = 10.1016/0168-9525(96)10019-6 | volume=12| doi-access = free }} and are normally found in one or very few instances per genome. Generally, owing to the homing mechanism, the gene encoding the endonuclease (the HEG, "homing endonuclease gene") is located within the recognition sequence which the enzyme cuts, thus interrupting the homing endonuclease recognition sequence and limiting DNA cutting only to sites that do not (yet) carry the HEG.

Prior to transmission, one allele carries the gene (HEG⁺) while the other does not (HEG⁻), and is therefore susceptible to being cut by the enzyme. Once the enzyme is synthesized, it breaks the chromosome in the HEG⁻ allele, initiating a response from the cellular DNA repair system. The damage is repaired using recombination, taking the pattern of the opposite, undamaged DNA allele, HEG⁺, that contains the gene for the endonuclease. Thus, the gene is copied to the allele that initially did not have it and it is propagated through successive generations.{{cite journal |vauthors=Burt A, Koufopanou V | title = Homing endonuclease genes: the rise and fall and rise again of a selfish element | journal = Curr Opin Genet Dev | issue = 6 | pages = 609–15 |date=December 2004 | pmid = 15531154 | doi = 10.1016/j.gde.2004.09.010 | volume=14}} This process is called "homing".

Homing endonucleases are always indicated with a prefix that identifies their genomic origin, followed by a hyphen: "I-" for homing endonucleases encoded within an intron, "PI-" (for "protein insert") for those encoded within an intein. Some authors have proposed using the prefix "F-" ("freestanding") for viral enzymes and other natural enzymes not encoded by introns nor inteins, and "H-" ("hybrid") for enzymes synthesized in a laboratory.{{cite journal |vauthors=Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL | title = Design, activity, and structure of a highly specific artificial endonuclease | journal = Mol. Cell | volume = 10 | issue = 4 | pages=895–905 |date=October 2002 | pmid=12419232 | doi=10.1016/S1097-2765(02)00690-1| doi-access=free }} Next, a three-letter name is derived from the binominal name of the organism, taking one uppercase letter from the genus name and two lowercase letters from the specific name. (Some mixing is usually done for hybrid enzymes.) Finally, a Roman numeral distinguishes different enzymes found in the same organism:

• PI-TliII ({{UniProt|P30317}}) is the second-identified enzyme encoded by an intein found in the archaea Thermococcus litoralis.{{cite journal |vauthors=Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y | title = Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae | journal = J Biol Chem | pmid = 2139027 | volume = 265 | issue = 12 |date=April 1990 | pages = 6726–33| doi = 10.1016/S0021-9258(19)39210-5 | doi-access = free }}{{cite journal |vauthors=Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH | title = Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase | journal = Science | pmid = 2146742 | volume = 250 | issue = 4981 |date=November 1990 | pages = 651–7 | doi = 10.1126/science.2146742| bibcode = 1990Sci...250..651K }}{{cite journal |vauthors=Perler FB, Comb DG, Jack WE, Moran LS, Qiang B, Kucera RB, Benner J, Slatko BE, Nwankwo DO, Hempstead SK, Carlow CK, Jannasch H | title = Intervening sequences in an Archaea DNA polymerase gene | journal = PNAS | pmid = 1608969 | volume = 89 | issue = 12 |date=June 1992 | pages = 5577–81 | doi = 10.1073/pnas.89.12.5577 | pmc=49335| bibcode = 1992PNAS...89.5577P | doi-access = free }}
• H-DreI ({{PDB|1MOW}}) is the first synthetic homing endonuclease, created in a laboratory from the enzymes I-DmoI ({{UniProt|P21505}}) and I-CreI ({{UniProt|P05725}}), taken respectively from Desulfurococcus mobilis and Chlamydomonas reinhardtii.{{cite journal |vauthors=Jurica MS, Monnat RJ, Stoddard BL | title = DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI | journal = Mol. Cell | volume = 2 | issue = 4 |date=October 1998 | pages = 469–76 | pmid = 9809068 | doi = 10.1016/S1097-2765(00)80146-X | url=http://depts.washington.edu/monnatws/pdf/1998_Jurica.pdf }}

Homing endonucleases differ from Type II restriction enzymes in the several respects:{{cite journal |vauthors=Belfort M, Roberts RJ| title = Homing endonucleases: keeping the house in order | journal = Nucleic Acids Res | volume = 25 | issue = 17 |date=September 1995 | pages = 3379–88 | pmid = 9254693 | doi = 10.1093/nar/25.17.3379 | pmc = 146926}}

• Whereas Type II restriction enzymes bind short, usually symmetric, recognition sequences of 4 to 8 bp, homing endonucleases bind very long and in many cases asymmetric recognition sequences spanning 12 to 40 bp.
• Homing endonucleases are generally more tolerant of substitutions in the recognition sequence. Minor variations in the recognition sequence usually decrease the activity of homing endonucleases, but often do not completely abolish it as often occurs with restriction enzymes.{{cite journal |vauthors=Gimble FS, Wang J | title = Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing | journal = J Mol Biol | volume = 263 | issue = 2 |date=October 1996 | pages = 163–80 | pmid = 8913299 | doi = 10.1006/jmbi.1996.0567 }}{{cite journal |vauthors=Argast GM, Stephens KM, Emond MJ, Monnat RJ | title = I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment | journal = J Mol Biol | volume = 280 | issue = 3 |date=July 1998 | pages = 345–53 | pmid = 9665841 | doi = 10.1006/jmbi.1998.1886 }}
• Homing endonucleases share structural motifs that suggest there are four families, whereas it has not been possible to determine simply recognisable and distinguishable families of Type II restriction enzymes.
• Homing endonucleases act as monomers or homodimers, and often require associated proteins to regulate their activity{{cite journal |vauthors=Shibata T, Nakagawa K, Morishima N | title = Multi-site-specific endonucleases and the initiation of homologous genetic recombination in yeast | journal = Adv Biophys | volume = 31 | pages = 77–91 | pmid = 7625280 | year = 1995 | doi = 10.1016/0065-227X(95)99384-2 }} or form ribonucleoprotein complexes, wherein RNA is an integral component of the catalytic apparatus.{{cite journal |vauthors=Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM | title = A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility | journal = Cell | volume = 83 | issue = 4 |date=November 1995 | pages = 529–38 | pmid = 7585955 | doi = 10.1016/0092-8674(95)90092-6 | s2cid = 10456475 | doi-access = free }} Type II restriction enzymes can also function alone, as monomers or homodimers,{{Cite book | last1 = Linn | first1 = Stuart M | last2 = Lloyd | first2 = R Stephen | last3 = Roberts | first3 = Richard J | title = Nucleases | publisher = Cold Spring Harbor Press |date=December 1993 | pages = 35–88 | isbn = 978-0-87969-426-5 }} or with additional protein subunits,{{Cite book | last1 = Linn | first1 = Stuart M | last2 = Lloyd | first2 = R Stephen | last3 = Roberts | first3 = Richard J | title = Nucleases | publisher = Cold Spring Harbor Press |date=December 1993 | pages = 89–109 | isbn = 978-0-87969-426-5 }} but the accessory subunits differ from those of the homing endonucleases. Thus, they can require restriction, modification, and specificity subunits for their action.
• Finally, homing endonucleases have a broader phylogenetic distribution, occurring in all three biological domains—the archaea, bacteria and eukarya. Type II restriction enzymes occur only in archaea, bacteria and certain viruses.{{cite journal|vauthors=Roberts RJ, Macelis D |title = REBASE-restriction enzymes and methylases|journal = Nucleic Acids Res|volume = 25|issue = 1|date=January 1997|pages = 248–62|pmid =9016548|doi=10.1093/nar/25.1.248|pmc=146408}}{{cite journal|vauthors=Lambowitz AM, Belfort M |title = Introns as mobile genetic elements|journal = Annu Rev Biochem|volume = 62|pages = 587–622|pmid = 8352597|year = 1993|doi = 10.1146/annurev.bi.62.070193.003103}}{{Cite book | last1 = Linn | first1 = Stuart M | last2 = Lloyd | first2 = R Stephen | last3 = Roberts | first3 = Richard J | title = Nucleases | publisher = Cold Spring Harbor Press |date=December 1993 | pages = 111–143 | isbn = 978-0-87969-426-5 }} Homing endonucleases are also expressed in all three compartments of the eukaryotic cell: nuclei, mitochondria and chloroplasts. Open reading frames encoding homing endonucleases have been found in introns, inteins, and in freestanding form between genes, whereas genes encoding Type II restriction enzyme genes have been found only in freestanding form, almost always in close association with genes encoding cognate DNA modifying enzymes.{{cite journal|author = Wilson GG | title = Cloned restriction-modification systems—a review | journal = Gene | volume = 74 |issue = 1 |date=December 1988 | pages = 281–9 | pmid = 3074014 | doi = 10.1016/0378-1119(88)90304-6}} Thus, while the Type II restriction enzymes and homing endonucleases share the function of cleaving double-stranded DNA, they appear to have evolved independently.

|}

{{Infobox protein family

| Symbol = LAGLIDADG_1

| Name = LAGLIDADG endonuclease

| image =

| width =

| caption =

| Pfam = PF00961

| Pfam_clan = CL0324

| InterPro = IPR001982

| SMART =

| PROSITE =

| MEROPS =

| SCOP = 1af5

| CATH = 1af5

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

| below = See clan entry for related Pfam families.

}}

{{Pfam box

|Name=GIY-YIG endonuclease, catalytic

|Pfam=PF01541

|Symbol=GIY-YIG

|InterPro=IPR000305

|PROSITE=PS50164

|SCOP=1mk0|CATH=1mk0}}

Currently there are six known structural families. Their conserved structural motifs are:

• LAGLIDADG: Every polypeptide has 1 or 2 LAGLIDADG motifs. The sequence LAGLIDADG is a conserved sequence of amino acids where each letter is a code that identifies a specific residue. This sequence is directly involved in the DNA cutting process. Those enzymes that have only one motif work as homodimers, creating a saddle that interacts with the major groove of each DNA half-site. The LAGLIDADG motifs contribute amino acid residues to both the protein-protein interface between protein domains or subunits, and to the enzyme's active sites. Enzymes that possess two motifs in a single protein chain act as monomers, creating the saddle in a similar way. The first structures to be determined of homing endonucleases (of PI-SceI and I-CreI, both reported in 1997) were both from the LAGLIDADG structural family.,{{cite journal | author = Heath, P. | title = The structure of I-Crel, a group I intron-encoded homing endonuclease | journal = Nature Structural Biology | volume = 4 | issue = 6 |date=June 1997 | pages = 468–476 | pmid = 9187655 | display-authors = 1 | doi = 10.1038/nsb0697-468 | last2 = Stephens | first2 = KM | last3 = Monnat Jr | first3 = RJ | last4 = Stoddard | first4 = BL| s2cid = 12261983 }}{{cite journal | author = Duan, X. | title = Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity | journal = Cell | volume = 89 | issue = 4 |date=May 1997 | pages = 555–564 | pmid = 9160747 | doi = 10.1016/S0092-8674(00)80237-8 | s2cid = 14156646 | doi-access = free }} The following year, the first structure of a homing endonuclease (I-CreI) bound to its DNA target site was also reported.
• GIY-YIG: These have only one GIY-YIG motif, in the N-terminal region, that interacts with the DNA in the cutting site. The prototypic enzyme of this family is I-TevI which acts as a monomer. Separate structural studies have been reported of the DNA-binding and catalytic domains of I-TevI, the former bound to its DNA target and the latter in the absence of DNA.{{cite journal |last1=Van Roey | title = Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate | journal = EMBO J. | volume = 20 | issue = 14 |date=July 2001 | pages = 3631–3637 | pmid = 11447104 | doi=10.1093/emboj/20.14.3631 | pmc=125541 |first1=P. | display-authors = 2 | last2 = Fox | first2 = KM | last3 = Belfort | first3 = M | last4 = Derbyshire | first4 = V}}{{cite journal |last1=Van Roey | title = Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI | journal = Nature Structural Biology | volume = 9 | issue = 11 |date=July 2002 | pages = 806–811 | pmid = 12379841 | doi=10.1038/nsb853 |first1=P. | display-authors = 2 | last2 = Kowalski | first2 = Joseph C. | last3 = Belfort | first3 = Marlene | last4 = Derbyshire | first4 = Victoria| s2cid = 24856337 }}
• His-Cys box ({{Pfam|PF05551}}): These enzymes possess a region of 30 amino acids that includes 5 conserved residues: two histidines and three cysteins. They co-ordinate the metal cation needed for catalysis. I-PpoI is the best characterized enzyme of this family and acts as a homodimer. Its structure was reported in 1998.{{cite journal | author = Flick, K. | title = DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI | journal = Nature | volume = 394 | issue = 6688 |date=July 1998 | pages = 96–101 | pmid = 9665136 | doi=10.1038/27952 | display-authors = 1 | last2 = Flick | first2 = Karen E. | last3 = Jurica | first3 = Melissa S. | last4 = Monnat | first4 = Raymond J.| bibcode = 1998Natur.394...96F | s2cid = 4427957 }} It is possibly related to the H-N-H family, as they share common features.{{cite journal |last1=Hafez |first1=M |last2=Hausner |first2=G |title=Homing endonucleases: DNA scissors on a mission. |journal=Genome |date=August 2012 |volume=55 |issue=8 |pages=553–69 |doi=10.1139/g2012-049 |pmid=22891613|doi-access= |s2cid=29183470 }}
• H-N-H: ({{Pfam|CL0263|clan}}): These have a consensus sequence of approximately 30 amino acids. It includes two pairs of conserved histidines and one asparagine that create a zinc finger domain. I-HmuI ({{UniProt|P34081}}) is the best characterized enzyme of this family, and acts as a monomer. Its structure was reported in 2004 ({{PDB|1U3E}}).{{cite journal | author = Shen, B.W. | title = DNA binding and cleavage by the HNH homing endonuclease I-HmuI | journal = J. Mol. Biol. | volume = 342 | issue = 1 |date=September 2004 | pages = 43–56 | pmid = 15313606 | doi=10.1016/j.jmb.2004.07.032 | display-authors = 1 | last2 = Landthaler | first2 = Markus | last3 = Shub | first3 = David A. | last4 = Stoddard | first4 = Barry L.| s2cid = 15990707 }}
• PD-(D/E)xK ({{Pfam|CL0236|clan}}): These enzymes contain a canonical nuclease catalytic domain typically found in type II restriction endonucleases. The best characterized enzyme in this family, I-Ssp6803I ({{UniProt|Q57253}}), acts as a tetramer. Its structure was reported in 2007 ({{PDB|2OST}}).{{cite journal | author = Zhao, L. | title = The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif | journal = EMBO Journal | volume = 26 | issue = 9 |date=May 2007 | pages = 2432–2442 | pmid = 17410205 | doi=10.1038/sj.emboj.7601672 | pmc=1864971 | display-authors = 1 | last2 = Bonocora | first2 = Richard P | last3 = Shub | first3 = David A | last4 = Stoddard | first4 = Barry L}} The overall fold is conserved in many endonuclease families, all of which belong to the PD-(D/E)xK superfamily.{{cite journal |last1=Steczkiewicz |first1=K |last2=Muszewska |first2=A |last3=Knizewski |first3=L |last4=Rychlewski |first4=L |last5=Ginalski |first5=K |title=Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. |journal=Nucleic Acids Research |date=August 2012 |volume=40 |issue=15 |pages=7016–45 |doi=10.1093/nar/gks382 |pmid=22638584|pmc=3424549 }}
• Vsr-like/EDxHD (DUF559, {{InterPro|IPR007569}}): These enzymes were discovered in the Global Ocean Sampling Metagenomic Database and first described in 2009. The term 'Vsr-like' refers to the presence of a C-terminal nuclease domain that displays recognizable homology to bacterial Very short patch repair (Vsr) endonucleases.{{cite journal | author = Dassa, B. | title = Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family | journal = Nucleic Acids Research | volume = 37 | issue = 8 |date=March 2009 | pages = 2560–2573 | pmid = 19264795 | doi=10.1093/nar/gkp095 | pmc=2677866 | display-authors = 1 | last2 = London | first2 = N. | last3 = Stoddard | first3 = B. L. | last4 = Schueler-Furman | first4 = O. | last5 = Pietrokovski | first5 = S.}} The structure has been solved in 2011, confirming the Vsr homology.{{cite journal |last1=Taylor |first1=GK |last2=Heiter |first2=DF |last3=Pietrokovski |first3=S |last4=Stoddard |first4=BL |title=Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. |journal=Nucleic Acids Research |date=December 2011 |volume=39 |issue=22 |pages=9705–19 |doi=10.1093/nar/gkr669 |pmid=21890897|pmc=3239194 }} Is considered part of the PD-(D/E)xk superfamily.

{{Infobox protein family

| Symbol = Hom_end_hint

| Name = Hom_end-associated Hint

| image = PDB 1ef0 EBI.jpg

| width =

| caption = crystal structure of pi-scei miniprecursor

| Pfam = PF05203

| Pfam_clan = CL0363

| InterPro = IPR007868

| SMART =

| PROSITE =

| MEROPS =

| SCOP = 1gpp

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

| below= Intein motif of the larger LAGLIDADG Hom_end domain.

}}

The yeast homing endonuclease PI-Sce is a LAGLIDADG-type endonuclease encoded as an intein that splices itself out of another protein ({{UniProt|P17255}}). The high-resolution structure reveals two domains: an endonucleolytic centre resembling the C-terminal domain of Hedgehog proteins, and a Hint domain (Hedgehog/Intein) containing the protein-splicing active site.{{cite journal |vauthors=Moure CM, Gimble FS, Quiocho FA | title = Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence | journal = Nat. Struct. Biol. | volume = 9 | issue = 10 | pages = 764–70 |date=October 2002 | pmid = 12219083 | doi = 10.1038/nsb840 | s2cid = 40192379 }}

• REBASE, a comprehensive restriction enzyme database from New England Biolabs with links to related literature.
• List of homing endonuclease cutting sites
• I-CreI homing endonuclease
• Meganucleases
• Restriction enzyme
• Introns and inteins
• Intragenomic conflict: Homing endonuclease genes
• Transposon

{{Reflist}}

• {{cite web| url =http://www.neb.com/neb/inteins.html| title =InBase| author =Perler FB| archive-url =https://web.archive.org/web/20100802024011/http://www.neb.com/neb/inteins.html| archive-date =2010-08-02| quote =The Intein Database and Registry (from New England Biolabs)| access-date =2010-08-09| url-status =dead}}
• {{cite journal | author = Perler FB | title = InBase: the Intein Database | journal = Nucleic Acids Res | volume = 30 | issue = 1 |date=January 2002 | pages = 383–4 | pmid = 11752343 | doi=10.1093/nar/30.1.383 | pmc=99080}}

{{InterPro content|IPR007868}}

{{InterPro content|IPR007869}}

{{DEFAULTSORT:Homing Endonuclease}}

Category:Protein domains

Category:Molecular biology

Category:Biotechnology

Category:Restriction enzymes